8dcg
From Proteopedia
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[8dcg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCG FirstGlance]. <br> | <table><tr><td colspan='2'>[[8dcg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCG FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.35Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8dcg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcg OCA], [https://pdbe.org/8dcg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcg RCSB], [https://www.ebi.ac.uk/pdbsum/8dcg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcg ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8dcg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcg OCA], [https://pdbe.org/8dcg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcg RCSB], [https://www.ebi.ac.uk/pdbsum/8dcg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcg ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| - | Pyrococcus horikoshii (Pho) RtcB exemplifies a family of binuclear transition metal- and GTP-dependent RNA ligases that join 3'-phosphate and 5'-OH ends via RtcB-(histidinyl-N)-GMP and | + | Pyrococcus horikoshii (Pho) RtcB exemplifies a family of binuclear transition metal- and GTP-dependent RNA ligases that join 3'-phosphate and 5'-OH ends via RtcB-(histidinyl-N)-GMP and RNA(3')pp(5')G intermediates. We find that guanylylation of PhoRtcB is optimal with manganese and less effective with cobalt and nickel. Zinc and copper are inactive and potently inhibit manganese-dependent guanylylation. We report crystal structures of PhoRtcB in complexes with GTP and permissive (Mn, Co, Ni) or inhibitory (Zn, Cu) metals. Zinc and copper occupy the M1 and M2 sites adjacent to the GTP phosphates, as do manganese, cobalt, and nickel. The identity/positions of enzymic ligands for M1 (His234, His329, Cys98) and M2 (Cys98, Asp95, His203) are the same for permissive and inhibitory metals. The differences pertain to: (i) the coordination geometries and phosphate contacts of the metals; and (ii) the orientation of the His404 nucleophile with respect to the GTP alpha-phosphate and pyrophosphate leaving group. M2 metal coordination geometry correlates with metal cofactor activity, whereby inhibitory Zn2 and Cu2 assume a tetrahedral configuration and contact only the GTP gamma-phosphate, whereas Mn2, Co2, and Ni2 coordination complexes are pentahedral and contact the beta- and gamma-phosphates. The His404-Nepsilon-Palpha-O(alpha-beta) angle is closer to apical in Mn (179 degrees ), Co (171 degrees ), and Ni (169 degrees ) structures than in Zn (160 degrees ) and Cu (155 degrees ) structures. The octahedral Mn1 geometry in our RtcB*GTP*Mn(2+) structure, in which Mn1 contacts alpha-, beta-, and gamma-phosphates, transitions to a tetrahedral configuration after formation of RtcB*(His404)-GMP*Mn(2+) and departure of pyrophosphate. |
Structures of RNA ligase RtcB in complexes with divalent cations and GTP.,Jacewicz A, Dantuluri S, Shuman S RNA. 2022 Nov;28(11):1509-1518. doi: 10.1261/rna.079327.122. Epub 2022 Sep 1. PMID:36130078<ref>PMID:36130078</ref> | Structures of RNA ligase RtcB in complexes with divalent cations and GTP.,Jacewicz A, Dantuluri S, Shuman S RNA. 2022 Nov;28(11):1509-1518. doi: 10.1261/rna.079327.122. Epub 2022 Sep 1. PMID:36130078<ref>PMID:36130078</ref> | ||
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</div> | </div> | ||
<div class="pdbe-citations 8dcg" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 8dcg" style="background-color:#fffaf0;"></div> | ||
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| + | ==See Also== | ||
| + | *[[RNA ligase|RNA ligase]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
Structure of guanylylated RNA ligase RtcB from Pyrococcus horikoshii
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